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- PDB-3cmx: Mechanism of homologous recombination from the RecA-ssDNA/dsDNA s... -

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Basic information

Entry
Database: PDB / ID: 3cmx
TitleMechanism of homologous recombination from the RecA-ssDNA/dsDNA structures
Components
  • DNA (5'-D(*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DA)-3')
  • DNA (5'-D(*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DT)-3')
  • Protein recA
Keywordsrecombination/DNA / homologous recombination / recombination-DNA COMPLEX
Function / homology
Function and homology information


DNA polymerase V complex / homologous recombination / recombinational repair / SOS response / ATP-dependent DNA damage sensor activity / response to ionizing radiation / translesion synthesis / ATP-dependent activity, acting on DNA / cell motility / single-stranded DNA binding ...DNA polymerase V complex / homologous recombination / recombinational repair / SOS response / ATP-dependent DNA damage sensor activity / response to ionizing radiation / translesion synthesis / ATP-dependent activity, acting on DNA / cell motility / single-stranded DNA binding / DNA-binding transcription factor binding / DNA recombination / damaged DNA binding / DNA damage response / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
RecA protein, C-terminal domain / Rec A Protein; domain 2 / : / : / RecA C-terminal domain / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / recA signature. / DNA recombination and repair protein RecA / recA bacterial DNA recombination protein ...RecA protein, C-terminal domain / Rec A Protein; domain 2 / : / : / RecA C-terminal domain / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / recA signature. / DNA recombination and repair protein RecA / recA bacterial DNA recombination protein / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / DNA / DNA (> 10) / Protein RecA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsPavletich, N.P.
CitationJournal: Nature / Year: 2008
Title: Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures.
Authors: Chen, Z. / Yang, H. / Pavletich, N.P.
History
DepositionMar 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DT)-3')
C: DNA (5'-D(*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DA)-3')
E: DNA (5'-D(*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DT)-3')
F: DNA (5'-D(*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DA)-3')
A: Protein recA
D: Protein recA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)386,48936
Polymers380,9446
Non-polymers5,54530
Water0
1
B: DNA (5'-D(*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DT)-3')
C: DNA (5'-D(*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DA)-3')
A: Protein recA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,24518
Polymers190,4723
Non-polymers2,77215
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (5'-D(*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DT)-3')
F: DNA (5'-D(*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DA)-3')
D: Protein recA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,24518
Polymers190,4723
Non-polymers2,77215
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.000, 300.500, 80.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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DNA chain , 2 types, 4 molecules BECF

#1: DNA chain DNA (5'-D(*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DT)-3')


Mass: 4517.935 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DA)-3')


Mass: 3713.524 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein , 1 types, 2 molecules AD

#3: Protein Protein recA / Recombinase A


Mass: 182240.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A7G6

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Non-polymers , 3 types, 30 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: AlF4
#6: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growpH: 8
Details: RecA5 fusion protein was incubated with a 3-fold molar excess of ssDNA in the original protein buffer supplemented with 2 mM ADP, 10 mM MgCl2 and 8 mM AlF4, pH 6.0. Crystals of the RecA5- ...Details: RecA5 fusion protein was incubated with a 3-fold molar excess of ssDNA in the original protein buffer supplemented with 2 mM ADP, 10 mM MgCl2 and 8 mM AlF4, pH 6.0. Crystals of the RecA5-(ADP-AlF4-Mg)5-(dT)15 complex were grown from 50 mM Tris-Cl, 9% (w/v) PVP K15, 32% (v/v) MPD, 10 mM DTT, pH 8.0. RecA5-(ADP-AlF4-Mg)5-(dT)15-(dA)12 complex were obtained by soaking the RecA5-(ADP-AlF4-Mg)5-(dT)15 crystals in a 0.2 mM solution of the complementary (dA)12 oligonucleotide in 25 mM Tris-Cl, 9% (w/v) PVP K15, 32% (v/v) MPD, 2 mM ADP, 8 mM AlF4, and 10 mM MgCl2 for 4 hr.
Components of the solutions
IDNameCrystal-IDSol-ID
1ADPAdenosine diphosphate11
2MgCl211
3AlF411
450 mM Tris-Cl11
5PVP K111
6MPD11
7DTT11
850 mM Tris-Cl12
9PVP K112
10MPD12
11DTT12
1225 mM Tris-Cl13
13PVP K1513
14MPD13
15ADPAdenosine diphosphate13
16AlF413
17MgCl213

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorDate: Feb 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.4→40 Å / Num. obs: 49365

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Processing

SoftwareName: REFMAC / Version: 5.3.0036 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→40 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.882 / SU B: 80.606 / SU ML: 0.579 / Cross valid method: THROUGHOUT / ESU R Free: 0.643 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1588 3.1 %RANDOM
Rwork0.238 ---
obs0.239 49365 94.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--0.1 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 3.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24166 963 330 0 25459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02225886
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1862.04535059
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.08353192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90525.394990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.105154594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.13115136
X-RAY DIFFRACTIONr_chiral_restr0.070.24020
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218489
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.211304
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.217418
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2750
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1550.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3880.2114
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3610.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8431.2516105
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.485225156
X-RAY DIFFRACTIONr_scbond_it1.499211087
X-RAY DIFFRACTIONr_scangle_it2.42239903
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.4→3.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 74 -
Rwork0.329 2763 -
obs--72.02 %

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